There is a huge potential for nutrient recovery from organic waste materials for soil fertility restoration as well as negative environmental emission mitigation. Previous research has found vermicomposting the optimal choice for converting organic waste into beneficial organic fertilizer while reducing reactive N loss. However, a great deal of the processes of greenhouse gases (GHG) and ammonia volatilization during vermicomposting are not well-documented. A field vermicomposting experiment was conducted by deploying earthworms (Eisenia fetida) with three types of agricultural by-products—namely, cow manure (VCM), pig manure (VPM), and biochar (VBC)—and crop (maize) residues compared with traditional composting (COM) without earthworms in the Sichuan Basin, China. Results showed that vermicomposting caused a decrease in electrical conductivity (EC) and total organic carbon (TOC) while increasing total nitrogen (TN). The greatest TN increase was found with VCM. The cumulative NH₃ volatilization in COM, VCM, VPM, and VBC during experimental duration was 9.00, 8.02, 15.16, and 8.91 kg N ha⁻¹, respectively. The cumulative CO₂ emissions in COM, VCM, VPM, and VBC were 2369, 2814, 3435, and 2984 (g·C·m⁻²), while for CH₄, they were 0.36, 0.28, 4.07, and 0.19 (g·C·m⁻²) and, for N₂O, they were 0.12, 0.06, 0.76, and 0.04 (g·N m⁻²), respectively. Lower emissions of N₂O, CH₄, and NH₃ were observed in VBC. We concluded that earthworms, as ecological engineers, enhanced reactive nutrients and reduced ammonia volatilization during vermicomposting in our test system. Overall, vermicomposting is proposed as an eco-friendly, sustainable technique that helps to reduce environmental impacts and associated health risks.